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Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
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Cryo-electron Microscopy01:28

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy.

Lin Chen1, Jing He2

  • 1Department of Computer Science, Valdosta State University, Valdosta, GA 31698.

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PubMed
Summary
This summary is machine-generated.

Cryo-electron microscopy (cryo-EM) structure quality has improved since 2017. Analysis shows better overall quality and conformation, with some exceptions in high-resolution datasets.

Keywords:
X-rayanomalycryo-electron microscopymachine learningprotein structureside-chainstatisticsvalidation

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Area of Science:

  • Structural Biology
  • Biophysics
  • Biochemistry

Background:

  • Cryo-electron microscopy (cryo-EM) is increasingly used to determine atomic structures.
  • Validating the quality of these cryo-EM structures is crucial.
  • Previous assessments of cryo-EM structure quality are limited.

Purpose of the Study:

  • To analyze changes in cryo-EM structure quality over time.
  • To compare structures released before and after December 2016.
  • To identify trends in conformational accuracy.

Main Methods:

  • Collected cryo-EM structures released between December 2016 and 2019.
  • Divided structures into six datasets based on resolution (better than 6 Å).
  • Applied a histogram-based outlier score (HBOS) and analyzed Protein Data Bank validation reports.

Main Results:

  • Cryo-EM structures released after December 2016 show improved overall quality compared to earlier ones.
  • Conformation quality generally improved for most residue types.
  • Exceptions were noted for Leucine, Phenylalanine, and Serine in high-resolution datasets (>4 Å).
  • Structures from 0-4 Å resolution maps showed similar HBOS profiles to those from 4-6 Å maps.

Conclusions:

  • The quality of atomic structures determined by cryo-EM has significantly improved.
  • Resolution is a key factor, but conformational accuracy shows nuanced changes.
  • Continued monitoring and validation are essential for advancing cryo-EM structural biology.